ArticleBMC genomics2009
The evolution of isochore patterns in vertebrate genomes.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2.BMC plant biology · 2023Article
- Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles.Animals : an open access journal from MDPI · 2023Review
- Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution.Genes · 2023Article
- On the Base Composition of Transposable Elements.International journal of molecular sciences · 2022Review
- Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1 and the acetylation of newly synthesized histones.Nucleic acids research · 2021Article
- Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution.Genes · 2021Article
- SALL4 controls cell fate in response to DNA base composition.Molecular cell · 2021Article
- Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts.Frontiers in microbiology · 2021Article
- Mobile Elements in Ray-Finned Fish Genomes.Life (Basel, Switzerland) · 2020Review
- IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.Genome biology and evolution · 2020Article
- Runaway GC Evolution in Gerbil Genomes.Molecular biology and evolution · 2020Article
- GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution.BMC evolutionary biology · 2019Article
- Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPrevious work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination.
resultsThe present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates.
conclusionOn the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection.
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